It would be a good idea to specify the exact flavor of markdown, as there are quite a few. I'm personally fond of Pandoc markdown since it has extensive features while also having excellent support for conversion through Pandoc, but the important thing is that we don't have everyone using their own personal favorite and assuming it'll just work while leaving client devs to come up with some sort of detection system so they can properly render random flavors.

I was intrigued to see AsciiDoc in the NIP as I was unfamiliar with it at the time, but the more I've looked at it and played with it, the less I like it for this. It doesn't read as nicely as markdown in raw form, it comes with a lot of features that don't make sense for individual articles themselves, and like you point out, the NIP isn't even compliant since wiki links override some of the anchor syntax. If it's gonna be markdown, though, there does need to be more effort to specify flavor. There are tons of options, but none of the NIPs I've seen for markdown styled content specify a flavor. I'm fond of Pandoc's markdown since it has a rich feature set and pairs with a high quality conversion tool, but the important thing is making sure everyone is on the same page.